Introduction

Introduction

This database hosts up-to-date annotation information of the genome of the methylotrophic yeast
Pichia pastoris (Komagataella spp.), containing the new manually achieved annotation of K. phaffii
strain CBS7435, and basic sequence and annotation information taken from the GenBank data of
various Komagataella strains and species. Additionally the sequence information of S. cerevisiae
strain S288c is also available for comparison and homolog display. A JBrowse based genome browser
is integrated into the annotation data website, displaying ORF annotation information, RNA-Seq data
and flanking regions of particular features.

Taxonomy and natural isolates of Pichia pastoris

TextTaxonomy

Pichia pastoris was first isolated in 1920 from the exudate of a chestnut tree in France, and described by A. Guilliermond as Zygosaccharomyces pastori [1]. This isolate is the species type strain, CBS704, (= NRRL Y-1603) [1]. Further strains were isolated from trees in California by H. Phaff, who named the species Pichia pastoris in 1956 [2]. For several decades, only few isolates existed, of which the strain NRRL Y-11430 (CBS7435), isolated from black oak tree in California, was developed as a platform for single cell protein by Philips Petroleum. This strain was then used as a basis for a development of the protein production system [3].Based on ribosomal gene sequence data, P. pastoris was re-classified in 1995 into a new phylogenetically distinct genus, Komagataella [4], which was later split into several species based on 26S rRNA sequencing data [5]. Currently six members of the genus Komagataella are described (K. pastoris, K. phaffii, K. pseudopastoris, K. poluli, K. ulmi, and K. kurtzmanii) [6]. The established Pichia pastoris protein production platforms are based on strains of either K. phaffii or K. pastoris [7]. According to the rules of biological taxonomy, the former type strain of the species P. pastoris CBS704 (NRRL Y-1603) remains the type strain of the genus Komagataella and of the species K. pastoris. The Californian isolates mentioned above differ enough in their 26S rRNA sequence to justify their allocation to a new species, K. phaffii [5]. Whole genome sequencing of K. pastoris CBS704 and K. phaffii CBS7435 ([8 – 10]) confirmed the presence of four chromosomes and a chromosome rearrangement between K. pastoris and K. phaffii, as identified by pulsed field gel electrophoresis [11]. It should be noted however that the members of the genus Komagataella are phenotypically very similar and cannot easily be distinguished from one another by routine fermentation and assimilation tests employed in yeast taxonomy, so that classification is mainly based on sequence comparisons of a limited number of genes. To avoid confusion and to include all strains employed in biotechnology we use the established name Pichia pastoris here as a synonym for all Komagataella species, giving reference to the different species for different strains, as listed in the table below.

*Please note that in some databases and strain collections species names have not been updated yet, and the species name is still Pichia pastoris. In some cases, K. phaffii has erroneously been named K. pastoris.